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Ok, thanks! I forgot to mention ut before, but this error only occurs when running it in IOS, in Linux it works fine...
El dv., 14 de maig 2021, 22:52, Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> va escriure:
Yes, but that doesn’t guarantee that the (library) environment is the same as when you run something from the terminal. I’m CCing Andrew Hoppes to see if he can assist. Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://secure-web.cisco.com/1mA1N83HM7Rsjl2L1KkalgrABlubZqRZ_UQ64lxXmRndx271...
On May 14, 2021, at 15:22, Joana Collet i Fàbregas joana.collet@gmail.com wrote:
External Email - Use CautionDear Juan Eugenio,
I'm not sure what you mean. In Python I use os.system() to run the recon-all command from the command line. Thanks!
Joana
El dv., 14 de maig 2021, 21:04, Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> va escriure:
Dear Joana, Is it possibly that Python changes somehow that libraries that are loaded, compared with the command line? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1mA1N83HM7Rsjl2L1KkalgrABlubZqRZ_UQ64lxXmRndx271... http://secure-web.cisco.com/148BToGpABivasWCgZR8rJMojzoD19lp4xSo0ku22rTNs46gi8eSQpxJJP6k6M4j5RKqRIKorP1-NtqedAacoQmEWnd8tz7Vpdfvp4n5xyzeV6jiUsTOjsuVZzv-qlc7NyV8dUlH8F8-il7vz5LfdbM8Fc5cE8WMR7k-VMx3r06GDDpq7BuAYFAW3uP54OD40bss37bbnQbVpyCeoZ7nJBWZdd6OefdWUCyQhy6OO9JK6dBHQjwvzXZyflpzJfxOHuNuGSCJc9x6KB1mnmc5tdw/http%3A%2F%2Fwww.jeiglesias.com
On May 14, 2021, at 06:06, Joana Collet i Fàbregas < joana.collet@gmail.com> wrote:
External Email - Use CautionGood morning,
I am a Biomedical Engineering Student at Universitat de Barcelona and I am creating a python script that has a Watchdog which detects new patients in a specific folder, and we want it to run FS and Hippocampal Subfields. The FS runs properly, but when the script arrives to the Hippocampal Subfields command, it breaks.
When using the FreeSurfer's Hippocampal Subfields from a python script after running FS recon-all right before, the processing is not performed due to the error shown in the attatched file. However, when running the Hippocampal Subfields from the terminal it does work.
We have even tried to create a watchdog only for the Hippocampal Subfields, and when we move a folder obtained after running FS to a specific folder, it also runs properly. It is only when it is concatenated with FS that it does not work.
We have contacted MathWorks Support, but they told us to reach you. The Matlab versions we have are Matlab_R2020a and Matlab_R2014b.
Thanks a lot,
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